SMTL ID : 1on3.1 (1 other biounit)

Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core (with methylmalonyl-coenzyme a and methylmalonic acid bound)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

3 x CD: CADMIUM ION(Non-covalent)

CD.1: 2 residues within 4Å: Chain A: H.387 Chain D: H.387 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: A:H.387, D:H.387, H2O.10, H2O.10, H2O.74, H2O.74 CD.5: 2 residues within 4Å: Chain B: H.387 Chain E: H.387 6 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: E:H.387, B:H.387, H2O.31, H2O.92, H2O.94, H2O.96 CD.9: 2 residues within 4Å: Chain C: H.387 Chain F: H.387 6 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: F:H.387, C:H.387, H2O.53, H2O.53, H2O.117, H2O.117

6 x MCA: METHYLMALONYL-COENZYME A(Non-covalent)

MCA.2: 20 residues within 4Å: Chain A: R.34, F.104, M.107, G.108, S.110, G.140, G.141, A.142, R.143, I.144, Q.145, P.177, A.179, G.180, G.181 Chain D: G.412, G.413, V.438, M.439 Ligands: DXX.3 18 PLIP interactions: 6 interactions with chain D, 12 interactions with chain A Hydrophobic interactions: D:V.438, A:P.177 Hydrogen bonds: D:G.413, A:S.110, A:G.140, A:A.142, A:I.144, A:A.179, A:G.181 Water bridges: D:Y.411, D:S.414, D:S.414, D:V.438, A:R.34, A:Q.41, A:Q.145, A:A.182 Salt bridges: A:R.34 MCA.6: 19 residues within 4Å: Chain B: R.34, F.104, M.107, G.108, S.110, G.140, G.141, A.142, R.143, I.144, Q.145, P.177, G.180, G.181 Chain E: G.412, G.413, V.438, M.439 Ligands: DXX.7 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain E Hydrophobic interactions: B:P.177, E:V.438 Hydrogen bonds: B:G.140, B:G.140, B:A.142, B:I.144, B:Q.145, B:G.181, E:G.413 Water bridges: B:R.34, B:K.37, B:K.37, B:K.37, B:A.179, B:A.182, E:S.414, E:R.450 Salt bridges: B:R.34 MCA.10: 22 residues within 4Å: Chain C: R.34, F.104, M.107, G.108, S.110, G.140, G.141, A.142, R.143, I.144, Q.145, P.177, A.179, G.180, G.181 Chain F: G.412, G.413, V.438, M.439, V.447, R.450 Ligands: DXX.11 18 PLIP interactions: 12 interactions with chain C, 6 interactions with chain F Hydrophobic interactions: C:P.177, F:V.438 Hydrogen bonds: C:S.110, C:G.140, C:A.142, C:I.144, C:Q.145, C:A.179, C:G.181, F:G.413, F:R.450, F:R.450 Water bridges: C:K.37, C:K.37, C:A.182, F:S.414 Salt bridges: C:R.34, F:R.450 MCA.12: 21 residues within 4Å: Chain A: G.412, G.413, V.438, M.439, K.451 Chain D: R.34, F.104, M.107, G.108, S.110, G.140, G.141, A.142, R.143, I.144, Q.145, P.177, G.180, G.181, Q.206 Ligands: DXX.13 24 PLIP interactions: 16 interactions with chain D, 8 interactions with chain A Hydrophobic interactions: D:P.177, A:V.438 Hydrogen bonds: D:S.110, D:G.140, D:G.140, D:A.142, D:I.144, D:G.181, D:Q.206, A:G.413 Water bridges: D:K.37, D:K.37, D:K.37, D:Q.41, D:Q.145, D:A.182, A:Y.411, A:Y.411, A:S.414, A:S.414, A:V.438 Salt bridges: D:R.34, D:K.37, A:K.451 MCA.14: 20 residues within 4Å: Chain B: G.412, G.413, V.438, M.439, R.450 Chain E: R.34, F.104, M.107, G.108, S.110, G.140, A.142, R.143, I.144, Q.145, P.177, A.179, G.180, G.181 Ligands: DXX.15 20 PLIP interactions: 7 interactions with chain B, 13 interactions with chain E Hydrophobic interactions: B:V.438, E:P.177 Hydrogen bonds: B:G.413, B:R.450, B:R.450, E:G.140, E:A.142, E:I.144, E:Q.145, E:A.179, E:G.181 Water bridges: B:S.414, B:S.414, E:K.37, E:K.37, E:Q.41, E:M.107, E:A.182 Salt bridges: B:R.450, E:R.34 MCA.16: 20 residues within 4Å: Chain C: G.412, G.413, V.438, M.439, V.447, R.450 Chain F: R.34, F.104, M.107, G.108, S.110, G.140, G.141, A.142, R.143, I.144, Q.145, P.177, G.180, G.181 22 PLIP interactions: 13 interactions with chain F, 9 interactions with chain C Hydrophobic interactions: F:P.177, C:V.438 Hydrogen bonds: F:G.140, F:G.140, F:A.142, F:I.144, F:Q.145, F:G.181, C:G.413 Water bridges: F:K.37, F:K.37, F:Q.41, F:Y.154, F:A.182, C:Y.411, C:S.414, C:V.438, C:R.450, C:K.451 Salt bridges: F:R.34, C:R.450, C:R.450

6 x DXX: METHYLMALONIC ACID(Non-covalent)

DXX.3: 5 residues within 4Å: Chain A: T.203, G.204, V.207 Chain D: M.439 Ligands: MCA.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:T.203, A:V.207 Hydrogen bonds: A:G.204 Water bridges: D:G.440 DXX.7: 4 residues within 4Å: Chain B: T.203, G.204, V.207 Ligands: MCA.6 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B Water bridges: E:V.438 Hydrophobic interactions: B:V.207 Hydrogen bonds: B:G.204 DXX.11: 4 residues within 4Å: Chain C: T.203, G.204, V.207 Ligands: MCA.10 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:V.207 Hydrogen bonds: C:G.204 Water bridges: C:G.181, F:V.438 DXX.13: 5 residues within 4Å: Chain D: I.202, T.203, G.204, V.207 Ligands: MCA.12 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.204 Water bridges: D:G.181, D:V.207 DXX.15: 7 residues within 4Å: Chain B: M.439 Chain E: G.180, I.202, T.203, G.204, V.207 Ligands: MCA.14 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.204 DXX.17: 5 residues within 4Å: Chain C: M.439 Chain F: I.202, T.203, G.204, V.207 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:T.203 Hydrogen bonds: F:G.204

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 4 residues within 4Å: Chain A: K.250, N.267, W.302, D.304 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.302 Hydrogen bonds: A:N.267, A:W.302 Water bridges: A:K.250 MPD.8: 5 residues within 4Å: Chain B: K.250, V.266, N.267, W.302, D.304 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:D.304 Hydrogen bonds: B:W.302 MPD.18: 4 residues within 4Å: Chain F: K.250, N.267, W.302, D.304 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:W.302 Water bridges: F:W.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hall, P.R. et al., Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core. Embo J. (2003)

Release Date

2003-05-20

Peptides

Methylmalonyl-CoA carboxyltransferase 12S subunit: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Methylmalonyl-CoA carboxyltransferase 12S subunit

Related Entries With Identical Sequence